Coronavirus ORF3a

Our protein folding group, Fold.it, University of Washington, is giving us known sequences of coronavirus protein to figure out its geometry.

Instructions from the group read as follows: The viral genome of SARS-CoV-2 encodes its proteins. This portion of a protein in SARS-CoV-2 is encoded in a region of the genome called ORF3a, but the protein’s structure and function are still unknown. If scientists knew how this protein folds, they might be able to figure out its function. The image shows SS (secondary structures) predictions from PSIPRED (a website devoted to predicting likely protein folds from known sequences) and hints which parts of the protein might fold into helices or sheets. Refolding this protein helps scientists to find possible conformations, which tell us how this protein is most likely to fold!

Sequence of amino acids in the protein:

WKCRSKNPLLYDANYFLCWHTNCYDYCIPYNSVTSSIVITSGDGTTSPISEHDYQIGGYTEKWESGVKDCVVLHSYFTSDYYQLYSTQLSTDTGVEHVTFFIYNKIVDEPEEHVQIHTIDGSSGVVNPVMEPIYDEPTTTTSVPL

There are twenty amino acids; each letter represents a different amino acid in the sequence.

For each unique sequence of amino acids, there is a uniquely folded protein, a basic tenet of protein folding.

The point of this exercise is to figure out the geometry of the coronavirus proteins. Knowing that is the first step in devising cures, treatments, vaccines, or medications that can stop the spread and devastation caused by this virus.

Published by Allen Lubow

Inventor, critical thinking.

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